PAF1_YEAST
ID PAF1_YEAST Reviewed; 445 AA.
AC P38351; D6VQS4; Q9URC9;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 194.
DE RecName: Full=RNA polymerase II-associated protein 1;
DE AltName: Full=Protein PAF1;
GN Name=PAF1; OrderedLocusNames=YBR279W; ORFNames=YBR2016;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091861; DOI=10.1002/yea.320100007;
RA Holmstroem K., Brandt T., Kallesoe T.;
RT "The sequence of a 32,420 bp segment located on the right arm of chromosome
RT II from Saccharomyces cerevisiae.";
RL Yeast 10:S47-S62(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP PROTEIN SEQUENCE OF 5-11 AND 419-426.
RX PubMed=8812838; DOI=10.1006/prep.1996.0077;
RA Wade P.A., Werel W., Fentzke R.C., Thompson N.E., Leykam J.F.,
RA Burgess R.R., Jaehning J.A., Burton Z.F.;
RT "A novel collection of accessory factors associated with yeast RNA
RT polymerase II.";
RL Protein Expr. Purif. 8:85-90(1996).
RN [5]
RP IDENTIFICATION, AND CHARACTERIZATION.
RX PubMed=8552095; DOI=10.1128/mcb.16.2.669;
RA Shi X., Finkelstein A., Wolf A.J., Wade P.A., Burton Z.F., Jaehning J.A.;
RT "Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae,
RT may have both positive and negative roles in transcription.";
RL Mol. Cell. Biol. 16:669-676(1996).
RN [6]
RP FUNCTION, AND SUBUNIT.
RX PubMed=10219085; DOI=10.1093/nar/27.10.2126;
RA Koch C., Wollmann P., Dahl M., Lottspeich F.;
RT "A role for Ctr9p and Paf1p in the regulation of G1 cyclin expression in
RT yeast.";
RL Nucleic Acids Res. 27:2126-2134(1999).
RN [7]
RP IDENTIFICATION IN THE PAF1 COMPLEX.
RX PubMed=11884586; DOI=10.1128/mcb.22.7.1971-1980.2002;
RA Mueller C.L., Jaehning J.A.;
RT "Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II
RT complex.";
RL Mol. Cell. Biol. 22:1971-1980(2002).
RN [8]
RP INTERACTION WITH POB3 AND SPT16.
RX PubMed=12242279; DOI=10.1128/mcb.22.20.6979-6992.2002;
RA Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A.,
RA Shilatifard A., Buratowski S., Greenblatt J.F.;
RT "RNA polymerase II elongation factors of Saccharomyces cerevisiae: a
RT targeted proteomics approach.";
RL Mol. Cell. Biol. 22:6979-6992(2002).
RN [9]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [10]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=15643076; DOI=10.1128/ec.4.1.209-220.2005;
RA Porter S.E., Penheiter K.L., Jaehning J.A.;
RT "Separation of the Saccharomyces cerevisiae Paf1 complex from RNA
RT polymerase II results in changes in its subnuclear localization.";
RL Eukaryot. Cell 4:209-220(2005).
RN [11]
RP FUNCTION.
RX PubMed=16246725; DOI=10.1016/j.molcel.2005.08.026;
RA Sheldon K.E., Mauger D.M., Arndt K.M.;
RT "A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3'
RT end formation.";
RL Mol. Cell 20:225-236(2005).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147 AND THR-422, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: The PAF1 complex is a multifunctional complex. Involved in
CC transcription initiation via genetic interactions with TATA-binding
CC proteins. Involved in elongation. It regulates 3'-end formation of
CC snR47 by modulating the recruitment or stable association of NRD1 and
CC NAB3 with RNA polymerase II. Also has a role in transcription-coupled
CC histone modification. Required for activation of the RAD6/UBC2-BRE1
CC ubiquitin ligase complex, which ubiquitinates histone H2B to form
CC H2BK123ub1. Also required for the methylation of histone H3 by the
CC COMPASS complex to form H3K4me, by SET2 to form H3K36me, and by DOT1 to
CC form H3K79me. RNA polymerase II associated protein important for
CC transcription of a subset of genes. Required for both positive and
CC negative regulation. Negatively regulates MAK16 expression. Also
CC required for efficient CLN2 transcription in late G1 and may be
CC involved in transcription of galactose-inducible genes.
CC {ECO:0000269|PubMed:10219085, ECO:0000269|PubMed:15643076,
CC ECO:0000269|PubMed:16246725}.
CC -!- SUBUNIT: Component of the PAF1 complex which consists of at least
CC CDC73, CTR9, LEO1, PAF1 and RTF1. Interacts with FACT subunits POB3 and
CC SPT16. {ECO:0000269|PubMed:10219085, ECO:0000269|PubMed:11884586,
CC ECO:0000269|PubMed:12242279}.
CC -!- INTERACTION:
CC P38351; Q06697: CDC73; NbExp=8; IntAct=EBI-12855, EBI-29913;
CC P38351; P89105: CTR9; NbExp=5; IntAct=EBI-12855, EBI-5283;
CC P38351; P38439: LEO1; NbExp=5; IntAct=EBI-12855, EBI-10108;
CC P38351; P53064: RTF1; NbExp=8; IntAct=EBI-12855, EBI-16303;
CC P38351; Q00772: SLT2; NbExp=2; IntAct=EBI-12855, EBI-17372;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:15643076}.
CC -!- MISCELLANEOUS: Present with 1040 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the PAF1 family. {ECO:0000305}.
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DR EMBL; X76053; CAA53642.1; -; Genomic_DNA.
DR EMBL; Z36148; CAA85243.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07394.1; -; Genomic_DNA.
DR PIR; S44541; S44541.
DR RefSeq; NP_009838.1; NM_001178627.1.
DR PDB; 5ZYP; X-ray; 2.53 A; A=34-103.
DR PDB; 7DKH; X-ray; 2.90 A; B/F/J=1-103.
DR PDBsum; 5ZYP; -.
DR PDBsum; 7DKH; -.
DR AlphaFoldDB; P38351; -.
DR SMR; P38351; -.
DR BioGRID; 32973; 176.
DR ComplexPortal; CPX-1726; PAF1 complex.
DR DIP; DIP-1149N; -.
DR IntAct; P38351; 11.
DR MINT; P38351; -.
DR STRING; 4932.YBR279W; -.
DR iPTMnet; P38351; -.
DR MaxQB; P38351; -.
DR PaxDb; P38351; -.
DR PRIDE; P38351; -.
DR EnsemblFungi; YBR279W_mRNA; YBR279W; YBR279W.
DR GeneID; 852582; -.
DR KEGG; sce:YBR279W; -.
DR SGD; S000000483; PAF1.
DR VEuPathDB; FungiDB:YBR279W; -.
DR eggNOG; KOG2478; Eukaryota.
DR HOGENOM; CLU_021991_3_1_1; -.
DR InParanoid; P38351; -.
DR OMA; MRPDGIY; -.
DR BioCyc; YEAST:G3O-29199-MON; -.
DR Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SCE-75955; RNA Polymerase II Transcription Elongation.
DR PRO; PR:P38351; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38351; protein.
DR GO; GO:0016593; C:Cdc73/Paf1 complex; IPI:SGD.
DR GO; GO:0000791; C:euchromatin; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IDA:SGD.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IPI:SGD.
DR GO; GO:0006353; P:DNA-templated transcription, termination; IMP:SGD.
DR GO; GO:0070911; P:global genome nucleotide-excision repair; IMP:SGD.
DR GO; GO:0016571; P:histone methylation; IC:ComplexPortal.
DR GO; GO:0031124; P:mRNA 3'-end processing; IMP:SGD.
DR GO; GO:0045910; P:negative regulation of DNA recombination; IMP:SGD.
DR GO; GO:1901525; P:negative regulation of mitophagy; IMP:SGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:2001255; P:positive regulation of histone H3-K36 trimethylation; IMP:SGD.
DR GO; GO:2001165; P:positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues; IMP:SGD.
DR GO; GO:2001209; P:positive regulation of transcription elongation from RNA polymerase I promoter; IDA:SGD.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IMP:SGD.
DR GO; GO:0000183; P:rDNA heterochromatin assembly; IMP:SGD.
DR GO; GO:2001173; P:regulation of histone H2B conserved C-terminal lysine ubiquitination; IDA:SGD.
DR GO; GO:2001166; P:regulation of histone H2B ubiquitination; IMP:SGD.
DR GO; GO:0051569; P:regulation of histone H3-K4 methylation; IMP:SGD.
DR GO; GO:2001163; P:regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues; IMP:SGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0000083; P:regulation of transcription involved in G1/S transition of mitotic cell cycle; IMP:SGD.
DR GO; GO:0090262; P:regulation of transcription-coupled nucleotide-excision repair; IGI:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR GO; GO:0031126; P:sno(s)RNA 3'-end processing; IMP:SGD.
DR GO; GO:0001015; P:snoRNA transcription by RNA polymerase II; IDA:SGD.
DR GO; GO:0006360; P:transcription by RNA polymerase I; IMP:SGD.
DR GO; GO:0006383; P:transcription by RNA polymerase III; IMP:SGD.
DR GO; GO:0006362; P:transcription elongation from RNA polymerase I promoter; IMP:SGD.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IMP:SGD.
DR InterPro; IPR007133; RNA_pol_II-assoc_Paf1.
DR PANTHER; PTHR23188; PTHR23188; 1.
DR Pfam; PF03985; Paf1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; Direct protein sequencing; Nucleus;
KW Phosphoprotein; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..445
FT /note="RNA polymerase II-associated protein 1"
FT /id="PRO_0000058174"
FT REGION 358..445
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 360..375
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 376..445
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 147
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 422
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:7DKH"
FT HELIX 43..56
FT /evidence="ECO:0007829|PDB:5ZYP"
FT TURN 60..63
FT /evidence="ECO:0007829|PDB:5ZYP"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:5ZYP"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:5ZYP"
FT HELIX 81..84
FT /evidence="ECO:0007829|PDB:5ZYP"
FT HELIX 93..96
FT /evidence="ECO:0007829|PDB:5ZYP"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:5ZYP"
SQ SEQUENCE 445 AA; 51801 MW; 46FB5AB37C3C1AAE CRC64;
MSKKQEYIAP IKYQNSLPVP QLPPKLLVYP ESPETNADSS QLINSLYIKT NVTNLIQQDE
DLGMPVDLMK FPGLLNKLDS KLLYGFDNVK LDKDDRILLR DPRIDRLTKT DISKVTFLRR
TEYVSNTIAA HDNTSLKRKR RLDDGDSDDE NLDVNHIISR VEGTFNKTDK WQHPVKKGVK
MVKKWDLLPD TASMDQVYFI LKFMGSASLD TKEKKSLNTG IFRPVELEED EWISMYATDH
KDSAILENEL EKGMDEMDDD SHEGKIYKFK RIRDYDMKQV AEKPMTELAI RLNDKDGIAY
YKPLRSKIEL RRRRVNDIIK PLVKEHDIDQ LNVTLRNPST KEANIRDKLR MKFDPINFAT
VDEEDDEDEE QPEDVKKESE GDSKTEGSEQ EGENEKDEEI KQEKENEQDE ENKQDENRAA
DTPETSDAVH TEQKPEEEKE TLQEE
